Starting phenix.real_space_refine on Fri Feb 14 19:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fpg_29363/02_2025/8fpg_29363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fpg_29363/02_2025/8fpg_29363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fpg_29363/02_2025/8fpg_29363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fpg_29363/02_2025/8fpg_29363.map" model { file = "/net/cci-nas-00/data/ceres_data/8fpg_29363/02_2025/8fpg_29363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fpg_29363/02_2025/8fpg_29363.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 72 5.16 5 Cl 4 4.86 5 C 6927 2.51 5 N 1657 2.21 5 O 2014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10674 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1456 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 185} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1157 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 148, 1146 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 1164 Chain: "B" Number of atoms: 1165 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 149, 1154 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 1172 Chain: "A" Number of atoms: 1152 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 148, 1141 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1159 Chain: "D" Number of atoms: 1161 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 149, 1150 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 1168 Chain: "E" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1468 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 186} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N APHE C 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 623 " occ=0.50 residue: pdb=" N APHE B 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 623 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 8.90, per 1000 atoms: 0.83 Number of scatterers: 10674 At special positions: 0 Unit cell: (108.994, 105.716, 92.6035, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 72 16.00 O 2014 8.00 N 1657 7.00 C 6927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.9 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 4 sheets defined 74.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'H' and resid 5 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 3.989A pdb=" N TYR H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 4.146A pdb=" N GLU H 126 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.737A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 214 Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.925A pdb=" N TYR F 96 " --> pdb=" O ASP F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 4.019A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.769A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 214 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.709A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 Processing helix chain 'C' and resid 547 through 551 Processing helix chain 'C' and resid 572 through 586 Processing helix chain 'C' and resid 595 through 629 Processing helix chain 'C' and resid 788 through 791 Processing helix chain 'C' and resid 792 through 825 removed outlier: 3.619A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.572A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 Processing helix chain 'B' and resid 547 through 551 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 Processing helix chain 'B' and resid 788 through 791 Processing helix chain 'B' and resid 792 through 825 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.711A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 629 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 825 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.574A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 Processing helix chain 'D' and resid 547 through 551 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 Processing helix chain 'D' and resid 788 through 791 Processing helix chain 'D' and resid 792 through 825 removed outlier: 3.660A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 92 through 105 Processing helix chain 'E' and resid 105 through 125 Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.596A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 92 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.587A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 removed outlier: 3.895A pdb=" N VAL H 57 " --> pdb=" O GLY H 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 77 through 79 removed outlier: 3.947A pdb=" N VAL F 57 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'G' and resid 34 through 38 854 hydrogen bonds defined for protein. 2494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3155 1.34 - 1.46: 2703 1.46 - 1.58: 4779 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 10749 Sorted by residual: bond pdb=" CB MET E 200 " pdb=" CG MET E 200 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" CB MET G 200 " pdb=" CG MET G 200 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" CB MET H 200 " pdb=" CG MET H 200 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.95e-01 bond pdb=" CB MET F 200 " pdb=" CG MET F 200 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.41e-01 bond pdb=" CG MET G 200 " pdb=" SD MET G 200 " ideal model delta sigma weight residual 1.803 1.781 0.022 2.50e-02 1.60e+03 7.74e-01 ... (remaining 10744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 14387 1.83 - 3.66: 158 3.66 - 5.48: 17 5.48 - 7.31: 0 7.31 - 9.14: 3 Bond angle restraints: 14565 Sorted by residual: angle pdb=" C CYS H 40 " pdb=" N LYS H 41 " pdb=" CA LYS H 41 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.87e+00 angle pdb=" CA LEU A 542 " pdb=" CB LEU A 542 " pdb=" CG LEU A 542 " ideal model delta sigma weight residual 116.30 125.44 -9.14 3.50e+00 8.16e-02 6.82e+00 angle pdb=" CA LEU C 542 " pdb=" CB LEU C 542 " pdb=" CG LEU C 542 " ideal model delta sigma weight residual 116.30 125.36 -9.06 3.50e+00 8.16e-02 6.71e+00 angle pdb=" CA LEU E 98 " pdb=" CB LEU E 98 " pdb=" CG LEU E 98 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" C CYS F 40 " pdb=" N LYS F 41 " pdb=" CA LYS F 41 " ideal model delta sigma weight residual 121.54 125.50 -3.96 1.91e+00 2.74e-01 4.29e+00 ... (remaining 14560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5329 17.15 - 34.30: 559 34.30 - 51.45: 164 51.45 - 68.59: 39 68.59 - 85.74: 8 Dihedral angle restraints: 6099 sinusoidal: 2227 harmonic: 3872 Sorted by residual: dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual 93.00 121.57 -28.57 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP A 590 " pdb=" CB ASP A 590 " pdb=" CG ASP A 590 " pdb=" OD1 ASP A 590 " ideal model delta sinusoidal sigma weight residual -30.00 -88.27 58.27 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP C 590 " pdb=" CB ASP C 590 " pdb=" CG ASP C 590 " pdb=" OD1 ASP C 590 " ideal model delta sinusoidal sigma weight residual -30.00 -87.82 57.82 1 2.00e+01 2.50e-03 1.12e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1152 0.035 - 0.071: 393 0.071 - 0.106: 89 0.106 - 0.142: 13 0.142 - 0.177: 1 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CB ILE E 106 " pdb=" CA ILE E 106 " pdb=" CG1 ILE E 106 " pdb=" CG2 ILE E 106 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CA PHE H 107 " pdb=" N PHE H 107 " pdb=" C PHE H 107 " pdb=" CB PHE H 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PHE G 107 " pdb=" N PHE G 107 " pdb=" C PHE G 107 " pdb=" CB PHE G 107 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 1645 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 32 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C TYR E 32 " -0.029 2.00e-02 2.50e+03 pdb=" O TYR E 32 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP E 33 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR G 32 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TYR G 32 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR G 32 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP G 33 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE E 107 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO E 108 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 108 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 108 " 0.018 5.00e-02 4.00e+02 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 370 2.71 - 3.26: 10886 3.26 - 3.81: 18809 3.81 - 4.35: 22219 4.35 - 4.90: 37551 Nonbonded interactions: 89835 Sorted by model distance: nonbonded pdb=" OD1 ASN G 160 " pdb=" O HOH G 501 " model vdw 2.165 3.040 nonbonded pdb=" OD1 ASN E 160 " pdb=" O HOH E 501 " model vdw 2.167 3.040 nonbonded pdb=" O PHE A 579 " pdb=" O HOH A 901 " model vdw 2.169 3.040 nonbonded pdb=" O HOH D 911 " pdb=" O HOH D 920 " model vdw 2.172 3.040 nonbonded pdb=" O HOH C 923 " pdb=" O HOH B1001 " model vdw 2.174 3.040 ... (remaining 89830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 511 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'B' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 626 or (resid 627 and (name N or name CA or name C or name O or name CB )) or \ resid 628 through 629 or (resid 784 and (name N or name CA or name C or name O o \ r name CB )) or resid 785 through 825)) selection = (chain 'C' and (resid 511 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 622 or resid 624 through 626 o \ r (resid 627 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 28 through 629 or resid 784 through 812 or (resid 813 and (name N or name CA or \ name C or name O or name CB )) or resid 814 through 818 or (resid 819 through 82 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 821 through \ 825)) selection = (chain 'D' and ((resid 511 and (name N or name CA or name C or name O or name CB \ )) or resid 512 through 575 or (resid 576 and (name N or name CA or name C or n \ ame O or name CB )) or resid 577 through 593 or (resid 594 and (name N or name C \ A or name C or name O or name CB )) or resid 595 through 622 or resid 624 throug \ h 629 or (resid 784 and (name N or name CA or name C or name O or name CB )) or \ resid 785 through 825)) } ncs_group { reference = (chain 'E' and (resid 5 through 214 or resid 401)) selection = (chain 'F' and (resid 5 through 41 or resid 55 through 214 or resid 401)) selection = (chain 'G' and (resid 5 through 214 or resid 401)) selection = (chain 'H' and (resid 5 through 41 or resid 55 through 214 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.750 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10749 Z= 0.200 Angle : 0.490 9.141 14565 Z= 0.263 Chirality : 0.037 0.177 1648 Planarity : 0.003 0.031 1778 Dihedral : 16.030 85.743 3595 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 17.42 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.23), residues: 1312 helix: 3.19 (0.16), residues: 948 sheet: 0.46 (0.78), residues: 48 loop : -0.87 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 64 HIS 0.006 0.001 HIS E 132 PHE 0.017 0.002 PHE C 584 TYR 0.015 0.002 TYR C 523 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: E 11 LEU cc_start: 0.7721 (tp) cc_final: 0.7037 (tp) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 1.2036 time to fit residues: 223.4848 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 523 TYR Chi-restraints excluded: chain A residue 523 TYR Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 150 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS C 791 ASN E 79 GLN G 9 GLN G 79 GLN G 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135101 restraints weight = 23908.681| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.08 r_work: 0.3103 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10749 Z= 0.142 Angle : 0.445 8.302 14565 Z= 0.246 Chirality : 0.035 0.138 1648 Planarity : 0.003 0.034 1778 Dihedral : 4.115 42.513 1462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.04 % Allowed : 16.50 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.23), residues: 1312 helix: 3.93 (0.15), residues: 950 sheet: 1.01 (1.30), residues: 10 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 33 HIS 0.003 0.001 HIS E 132 PHE 0.014 0.001 PHE G 107 TYR 0.013 0.001 TYR H 181 ARG 0.002 0.000 ARG G 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.068 Fit side-chains REVERT: H 113 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7650 (mt) REVERT: F 113 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7634 (mt) outliers start: 33 outliers final: 6 residues processed: 176 average time/residue: 0.9907 time to fit residues: 191.7272 Evaluate side-chains 156 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 117 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 60 HIS H 199 HIS F 60 HIS F 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.187769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.132115 restraints weight = 24390.847| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.10 r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10749 Z= 0.247 Angle : 0.532 7.013 14565 Z= 0.297 Chirality : 0.039 0.150 1648 Planarity : 0.004 0.036 1778 Dihedral : 3.707 20.112 1444 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.59 % Allowed : 14.84 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.23), residues: 1312 helix: 3.63 (0.15), residues: 948 sheet: 1.77 (1.32), residues: 10 loop : -0.59 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 33 HIS 0.005 0.001 HIS E 60 PHE 0.018 0.002 PHE A 584 TYR 0.016 0.002 TYR D 549 ARG 0.003 0.000 ARG C 545 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.090 Fit side-chains REVERT: H 78 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6595 (tmmt) REVERT: H 113 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7700 (mt) REVERT: F 78 LYS cc_start: 0.6724 (OUTLIER) cc_final: 0.6482 (tmmt) REVERT: F 113 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7682 (mt) outliers start: 39 outliers final: 14 residues processed: 183 average time/residue: 1.1002 time to fit residues: 219.0472 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS G 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.190112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132499 restraints weight = 23839.050| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 3.23 r_work: 0.3069 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10749 Z= 0.152 Angle : 0.448 6.610 14565 Z= 0.252 Chirality : 0.036 0.130 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.441 17.208 1444 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.95 % Allowed : 15.67 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.23 (0.23), residues: 1312 helix: 3.94 (0.16), residues: 950 sheet: 0.69 (1.13), residues: 10 loop : -0.64 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 33 HIS 0.003 0.001 HIS G 205 PHE 0.012 0.001 PHE C 584 TYR 0.013 0.001 TYR H 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.167 Fit side-chains REVERT: H 78 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6607 (tmmt) REVERT: H 113 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7602 (mt) REVERT: F 113 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7593 (mt) outliers start: 32 outliers final: 11 residues processed: 176 average time/residue: 1.1700 time to fit residues: 223.0323 Evaluate side-chains 169 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 132 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.133398 restraints weight = 23993.963| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.27 r_work: 0.3079 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10749 Z= 0.136 Angle : 0.428 7.399 14565 Z= 0.240 Chirality : 0.035 0.123 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.318 17.021 1444 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.49 % Allowed : 16.04 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.38 (0.23), residues: 1312 helix: 4.05 (0.16), residues: 952 sheet: 0.66 (1.12), residues: 10 loop : -0.61 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.003 0.001 HIS E 132 PHE 0.010 0.001 PHE C 584 TYR 0.013 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.242 Fit side-chains REVERT: H 78 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6645 (tmmt) REVERT: H 113 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7591 (mt) REVERT: F 113 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7591 (mt) REVERT: C 589 CYS cc_start: 0.5750 (p) cc_final: 0.4531 (m) REVERT: A 589 CYS cc_start: 0.5750 (p) cc_final: 0.4532 (m) REVERT: G 149 ASN cc_start: 0.8025 (t0) cc_final: 0.7747 (t0) REVERT: G 209 ARG cc_start: 0.5256 (OUTLIER) cc_final: 0.5016 (mtp85) outliers start: 27 outliers final: 11 residues processed: 180 average time/residue: 1.1024 time to fit residues: 216.6324 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 50 optimal weight: 0.0060 chunk 86 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS F 199 HIS E 60 HIS E 132 HIS G 60 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.191413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135330 restraints weight = 29883.534| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.49 r_work: 0.3060 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10749 Z= 0.135 Angle : 0.431 7.654 14565 Z= 0.240 Chirality : 0.035 0.119 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.248 16.607 1442 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.76 % Allowed : 16.59 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.23), residues: 1312 helix: 4.06 (0.16), residues: 952 sheet: 0.75 (1.14), residues: 10 loop : -0.60 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.017 0.002 HIS E 60 PHE 0.010 0.001 PHE C 584 TYR 0.013 0.001 TYR F 181 ARG 0.001 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.262 Fit side-chains REVERT: C 589 CYS cc_start: 0.5717 (p) cc_final: 0.4528 (m) REVERT: A 589 CYS cc_start: 0.5706 (p) cc_final: 0.4518 (m) REVERT: E 11 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6533 (tp) REVERT: G 149 ASN cc_start: 0.7957 (t0) cc_final: 0.7739 (t0) REVERT: G 209 ARG cc_start: 0.5264 (OUTLIER) cc_final: 0.5014 (mtp85) outliers start: 30 outliers final: 15 residues processed: 174 average time/residue: 1.1372 time to fit residues: 214.8680 Evaluate side-chains 166 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.189733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132700 restraints weight = 29195.863| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.39 r_work: 0.3043 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10749 Z= 0.170 Angle : 0.467 8.215 14565 Z= 0.260 Chirality : 0.036 0.127 1648 Planarity : 0.003 0.036 1778 Dihedral : 3.389 17.793 1442 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.04 % Allowed : 16.31 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.23), residues: 1312 helix: 3.91 (0.16), residues: 950 sheet: 0.89 (1.15), residues: 10 loop : -0.59 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 33 HIS 0.004 0.001 HIS E 132 PHE 0.016 0.001 PHE A 531 TYR 0.014 0.001 TYR F 181 ARG 0.001 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 1.130 Fit side-chains REVERT: H 113 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7490 (mt) REVERT: H 199 HIS cc_start: 0.7852 (OUTLIER) cc_final: 0.7352 (m-70) REVERT: F 113 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7500 (mt) REVERT: F 199 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7342 (m-70) REVERT: C 589 CYS cc_start: 0.5868 (p) cc_final: 0.4647 (m) REVERT: A 589 CYS cc_start: 0.5875 (p) cc_final: 0.4663 (m) REVERT: E 11 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6542 (tp) REVERT: E 95 GLU cc_start: 0.5368 (tt0) cc_final: 0.4943 (mp0) REVERT: G 56 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4523 (mm-30) REVERT: G 209 ARG cc_start: 0.5324 (OUTLIER) cc_final: 0.5052 (mtp85) outliers start: 33 outliers final: 17 residues processed: 172 average time/residue: 1.1221 time to fit residues: 209.9136 Evaluate side-chains 174 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 209 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 52 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 42 optimal weight: 0.0670 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.191720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133971 restraints weight = 22052.642| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.25 r_work: 0.3091 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10749 Z= 0.133 Angle : 0.431 8.214 14565 Z= 0.240 Chirality : 0.035 0.121 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.251 16.499 1442 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.76 % Allowed : 16.87 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.23), residues: 1312 helix: 4.07 (0.16), residues: 952 sheet: 0.63 (1.12), residues: 10 loop : -0.61 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.003 0.001 HIS E 132 PHE 0.010 0.001 PHE G 180 TYR 0.012 0.001 TYR H 181 ARG 0.001 0.000 ARG E 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.072 Fit side-chains REVERT: H 199 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7272 (m-70) REVERT: F 199 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7270 (m-70) REVERT: C 589 CYS cc_start: 0.5824 (p) cc_final: 0.4590 (m) REVERT: A 589 CYS cc_start: 0.5824 (p) cc_final: 0.4589 (m) REVERT: E 11 LEU cc_start: 0.7054 (tp) cc_final: 0.6465 (tp) REVERT: E 95 GLU cc_start: 0.5203 (tt0) cc_final: 0.4839 (mp0) REVERT: G 11 LEU cc_start: 0.7025 (tp) cc_final: 0.6441 (tp) outliers start: 30 outliers final: 13 residues processed: 173 average time/residue: 1.1588 time to fit residues: 220.1723 Evaluate side-chains 165 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.132881 restraints weight = 29889.898| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.51 r_work: 0.3035 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10749 Z= 0.169 Angle : 0.468 7.920 14565 Z= 0.260 Chirality : 0.036 0.127 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.383 17.931 1442 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.40 % Allowed : 16.87 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.21 (0.23), residues: 1312 helix: 3.90 (0.16), residues: 950 sheet: 0.88 (1.16), residues: 10 loop : -0.58 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 33 HIS 0.004 0.001 HIS E 132 PHE 0.019 0.001 PHE C 531 TYR 0.014 0.001 TYR F 181 ARG 0.001 0.000 ARG A 545 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.109 Fit side-chains REVERT: H 113 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7514 (mt) REVERT: H 199 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7388 (m-70) REVERT: F 113 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7513 (mt) REVERT: F 199 HIS cc_start: 0.7898 (OUTLIER) cc_final: 0.7324 (m-70) REVERT: C 589 CYS cc_start: 0.5910 (p) cc_final: 0.4685 (m) REVERT: A 589 CYS cc_start: 0.5918 (p) cc_final: 0.4701 (m) REVERT: E 11 LEU cc_start: 0.7102 (tp) cc_final: 0.6506 (tp) REVERT: E 95 GLU cc_start: 0.5251 (tt0) cc_final: 0.4843 (mp0) REVERT: G 11 LEU cc_start: 0.7078 (tp) cc_final: 0.6510 (tp) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 1.0797 time to fit residues: 194.3636 Evaluate side-chains 167 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 113 ILE Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 38 optimal weight: 0.3980 chunk 44 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 124 optimal weight: 0.0470 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.192143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138920 restraints weight = 29539.775| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.35 r_work: 0.3070 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10749 Z= 0.129 Angle : 0.433 8.060 14565 Z= 0.240 Chirality : 0.035 0.125 1648 Planarity : 0.003 0.035 1778 Dihedral : 3.247 16.286 1442 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.12 % Allowed : 17.24 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.44 (0.23), residues: 1312 helix: 4.10 (0.16), residues: 952 sheet: 0.56 (1.13), residues: 10 loop : -0.59 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 178 HIS 0.004 0.001 HIS E 132 PHE 0.012 0.001 PHE E 141 TYR 0.012 0.001 TYR F 181 ARG 0.001 0.000 ARG E 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.898 Fit side-chains REVERT: H 199 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7326 (m-70) REVERT: F 199 HIS cc_start: 0.7909 (OUTLIER) cc_final: 0.7349 (m-70) REVERT: C 589 CYS cc_start: 0.5834 (p) cc_final: 0.4639 (m) REVERT: A 589 CYS cc_start: 0.5840 (p) cc_final: 0.4642 (m) REVERT: E 11 LEU cc_start: 0.7315 (tp) cc_final: 0.6683 (tp) REVERT: E 12 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7148 (mp) REVERT: G 11 LEU cc_start: 0.7092 (tp) cc_final: 0.6512 (tp) REVERT: G 102 ARG cc_start: 0.7743 (tpt90) cc_final: 0.7409 (tpt90) outliers start: 23 outliers final: 15 residues processed: 169 average time/residue: 1.0462 time to fit residues: 193.0039 Evaluate side-chains 168 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 199 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 199 HIS Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 117 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain G residue 10 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 196 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 5 optimal weight: 0.0170 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 132 HIS ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.192444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137781 restraints weight = 26530.134| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.20 r_work: 0.3092 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10749 Z= 0.126 Angle : 0.428 9.054 14565 Z= 0.236 Chirality : 0.035 0.130 1648 Planarity : 0.003 0.034 1778 Dihedral : 3.192 15.913 1442 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.94 % Allowed : 17.42 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.48 (0.23), residues: 1312 helix: 4.13 (0.16), residues: 952 sheet: 0.63 (1.16), residues: 10 loop : -0.57 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 33 HIS 0.004 0.001 HIS E 132 PHE 0.020 0.001 PHE A 531 TYR 0.011 0.001 TYR F 181 ARG 0.001 0.000 ARG E 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9248.17 seconds wall clock time: 163 minutes 21.70 seconds (9801.70 seconds total)